fix on dist.gene + a few man pages corrections

[ape.git] / ChangeLog

diff --git a/ChangeLog b/ChangeLog
index b6bffe8687b5bf9a7dc248c22ae7d5b7ed99725f..3a9c02b524c1387d98fd2ea31c3270c154f78a36 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,13 @@
+               CHANGES IN APE VERSION 2.3-1
+
+
+BUG FIXES
+
+    o dist.gene() failed on most occasions with the default
+      pairwise.deletion = FALSE.
+
+
+
                CHANGES IN APE VERSION 2.3
 
 
@@ -10,13 +20,30 @@ NEW FEATURES
     o The new function yule.time fits a user-defined time-dependent
       Yule model by maximum likelihood.
 
+    o The new function makeNodeLabel creates and/or modifies node
+      labels in a flexible way.
+
+    o read.tree() and write.tree() have been modified so that they can
+      handle individual tree names.
+
+    o plot.phylo() has a new argument 'edge.lty' that specifies the
+      types of lines used for the edges (plain, dotted, dashed, ...)
+
+    o phymltest() has been updated to work with PhyML 3.0.1.
+
 
 BUG FIXES
 
     o drop.tip() shuffled tip labels in some cases.
 
+    o drop.tip() did not handle node.label correctly.
+
     o is.ultrametric() now checks the ordering of the edge matrix.
 
+    o ace() sometimes returned negative values of likelihoods of
+      ancestral states (thanks to Dan Rabosky for solving this long
+      lasting bug).
+
 
 OTHER CHANGES